Molecular modellingMolecular modelling encompasses all methods, theoretical and computational, used to model or mimic the behaviour of molecules. The methods are used in the fields of computational chemistry, drug design, computational biology and materials science to study molecular systems ranging from small chemical systems to large biological molecules and material assemblies. The simplest calculations can be performed by hand, but inevitably computers are required to perform molecular modelling of any reasonably sized system.
Molecular design softwareMolecular design software is notable software for molecular modeling, that provides special support for developing molecular models de novo. In contrast to the usual molecular modeling programs, such as for molecular dynamics and quantum chemistry, such software directly supports the aspects related to constructing molecular models, including: Molecular graphics interactive molecular drawing and conformational editing building polymeric molecules, crystals, and solvated systems partial charges development g
Protein foldingProtein folding is the physical process where a protein chain is translated into its native three-dimensional structure, typically a "folded" conformation, by which the protein becomes biologically functional. Via an expeditious and reproducible process, a polypeptide folds into its characteristic three-dimensional structure from a random coil. Each protein exists first as an unfolded polypeptide or random coil after being translated from a sequence of mRNA into a linear chain of amino acids.
Gibbs free energyIn thermodynamics, the Gibbs free energy (or Gibbs energy as the recommended name; symbol ) is a thermodynamic potential that can be used to calculate the maximum amount of work, other than pressure-volume work, that may be performed by a thermodynamically closed system at constant temperature and pressure. It also provides a necessary condition for processes such as chemical reactions that may occur under these conditions. The Gibbs free energy is expressed as where p is pressure, T is the temperature, U is the internal energy, V is volume, H is the enthalpy, and S is the entropy.
Thermodynamic free energyIn thermodynamics, the thermodynamic free energy is one of the state functions of a thermodynamic system (the others being internal energy, enthalpy, entropy, etc.). The change in the free energy is the maximum amount of work that the system can perform in a process at constant temperature, and its sign indicates whether the process is thermodynamically favorable or forbidden. Since free energy usually contains potential energy, it is not absolute but depends on the choice of a zero point.
Surface energyIn surface science, surface free energy (also interfacial free energy or surface energy) quantifies the disruption of intermolecular bonds that occurs when a surface is created. In solid-state physics, surfaces must be intrinsically less energetically favorable than the bulk of the material (the atoms on the surface have more energy compared with the atoms in the bulk), otherwise there would be a driving force for surfaces to be created, removing the bulk of the material (see sublimation).
Surface tensionSurface tension is the tendency of liquid surfaces at rest to shrink into the minimum surface area possible. Surface tension is what allows objects with a higher density than water such as razor blades and insects (e.g. water striders) to float on a water surface without becoming even partly submerged. At liquid–air interfaces, surface tension results from the greater attraction of liquid molecules to each other (due to cohesion) than to the molecules in the air (due to adhesion). There are two primary mechanisms in play.
Protein domainIn molecular biology, a protein domain is a region of a protein's polypeptide chain that is self-stabilizing and that folds independently from the rest. Each domain forms a compact folded three-dimensional structure. Many proteins consist of several domains, and a domain may appear in a variety of different proteins. Molecular evolution uses domains as building blocks and these may be recombined in different arrangements to create proteins with different functions.
Protein fold classIn molecular biology, protein fold classes are broad categories of protein tertiary structure topology. They describe groups of proteins that share similar amino acid and secondary structure proportions. Each class contains multiple, independent protein superfamilies (i.e. are not necessarily evolutionarily related to one another). Four large classes of protein that are generally agreed upon by the two main structure classification databases (SCOP and CATH).
Clustering high-dimensional dataClustering high-dimensional data is the cluster analysis of data with anywhere from a few dozen to many thousands of dimensions. Such high-dimensional spaces of data are often encountered in areas such as medicine, where DNA microarray technology can produce many measurements at once, and the clustering of text documents, where, if a word-frequency vector is used, the number of dimensions equals the size of the vocabulary.
